splatter

This is the released version of splatter; for the devel version, see splatter.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Release (3.23)

Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

Author: Luke Zappia [aut, cre] (ORCID: ORCID: 0000-0001-7744-8565 , GitHub: lazappi), Belinda Phipson [aut] (ORCID: ORCID: 0000-0002-1711-7454 , GitHub: bphipson), Christina Azodi [ctb] (ORCID: ORCID: 0000-0002-6097-606X , GitHub: azodichr), Alicia Oshlack [aut] ORCID: 0000-0001-9788-5690

Maintainer: Luke Zappia <luke at lazappi.id.au>

Citation (from within R, enter citation("splatter")):

Luke Zappia, Belinda Phipson, Alicia Oshlack. splatter: Simple Simulation of Single-cell RNA Sequencing Data. doi:10.18129/B9.bioc.splatter, R package version 1.36.0, https://bioconductor.org/packages/splatter.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("splatter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("splatter")

Splat simulation parameters	HTML	R Script
splatPop simulation	HTML	R Script
An introduction to the Splatter package	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.36.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.0), SingleCellExperiment
Imports	BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, lifecycle, locfit, matrixStats, methods, rlang, S4Vectors, scrapper, scuttle, stats, SummarizedExperiment, utils, withr
System Requirements
URL	https://bioconductor.org/packages/splatter/ https://github.com/Oshlack/splatter http://oshlacklab.com/splatter/
Bug Reports	https://github.com/Oshlack/splatter/issues

Suggests	BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave
Linking To
Enhances
Depends On Me
Imports Me	BatChef
Suggests Me	anglemania, ccImpute, HVP, mastR, NewWave, scellpam, scone, scPCA, smartid
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	splatter_1.36.0.tar.gz
Windows Binary (x86_64)	splatter_1.36.0.zip
macOS Binary (big-sur-x86_64)	splatter_1.36.0.tgz
macOS Binary (sonoma-arm64)	splatter_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/splatter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/splatter
Package Short Url	https://bioconductor.org/packages/splatter/
Package Downloads Report	Download Stats